diff --git a/assembly/pom.xml b/assembly/pom.xml
index 0cf047b..94ae35b 100644
--- a/assembly/pom.xml
+++ b/assembly/pom.xml
@@ -3,12 +3,12 @@
4.0.0
org.bdgenomics.cannoli
- cannoli-parent_2.10
+ cannoli-parent-spark2_2.11
0.2.0-SNAPSHOT
../pom.xml
- cannoli-assembly_2.10
+ cannoli-assembly-spark2_2.11
jar
Cannoli_${scala.version.prefix}: Assembly
@@ -52,7 +52,7 @@
org.bdgenomics.cannoli
- cannoli-cli_${scala.version.prefix}
+ cannoli-cli-spark2_${scala.version.prefix}
compile
diff --git a/cli/pom.xml b/cli/pom.xml
index 8132655..c2fad3e 100644
--- a/cli/pom.xml
+++ b/cli/pom.xml
@@ -3,12 +3,12 @@
4.0.0
org.bdgenomics.cannoli
- cannoli-parent_2.10
+ cannoli-parent-spark2_2.11
0.2.0-SNAPSHOT
../pom.xml
- cannoli-cli_2.10
+ cannoli-cli-spark2_2.11
jar
Cannoli_${scala.version.prefix}: CLI
@@ -74,17 +74,17 @@
org.bdgenomics.adam
- adam-cli_${scala.version.prefix}
+ adam-cli-spark2_${scala.version.prefix}
compile
org.bdgenomics.cannoli
- cannoli-core_${scala.version.prefix}
+ cannoli-core-spark2_${scala.version.prefix}
compile
org.bdgenomics.utils
- utils-misc_${scala.version.prefix}
+ utils-misc-spark2_${scala.version.prefix}
test-jar
test
diff --git a/core/pom.xml b/core/pom.xml
index 769012a..2acb76f 100644
--- a/core/pom.xml
+++ b/core/pom.xml
@@ -3,12 +3,12 @@
4.0.0
org.bdgenomics.cannoli
- cannoli-parent_2.10
+ cannoli-parent-spark2_2.11
0.2.0-SNAPSHOT
../pom.xml
- cannoli-core_2.10
+ cannoli-core-spark2_2.11
jar
Cannoli_${scala.version.prefix}: Core
@@ -49,12 +49,12 @@
org.bdgenomics.adam
- adam-core_${scala.version.prefix}
+ adam-core-spark2_${scala.version.prefix}
compile
org.bdgenomics.utils
- utils-misc_${scala.version.prefix}
+ utils-misc-spark2_${scala.version.prefix}
test-jar
test
diff --git a/distribution/pom.xml b/distribution/pom.xml
index a5f9df7..10cce63 100644
--- a/distribution/pom.xml
+++ b/distribution/pom.xml
@@ -3,12 +3,12 @@
4.0.0
org.bdgenomics.cannoli
- cannoli-parent_2.10
+ cannoli-parent-spark2_2.11
0.2.0-SNAPSHOT
../pom.xml
- cannoli-distribution_2.10
+ cannoli-distribution-spark2_2.11
pom
Cannoli_${scala.version.prefix}: Distribution
diff --git a/pom.xml b/pom.xml
index 1cf4211..6a55585 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,7 +8,7 @@
org.bdgenomics.cannoli
- cannoli-parent_2.10
+ cannoli-parent-spark2_2.11
0.2.0-SNAPSHOT
pom
Cannoli_${scala.version.prefix}
@@ -17,10 +17,10 @@
2017
- 0.23.0
- 2.10.6
- 2.10
- 1.6.3
+ 0.24.0-SNAPSHOT
+ 2.11.12
+ 2.11
+ 2.2.1
UTF-8
UTF-8
[3.1.1,)
@@ -349,27 +349,27 @@
org.bdgenomics.adam
- adam-core_${scala.version.prefix}
+ adam-core-spark2_${scala.version.prefix}
${adam.version}
org.bdgenomics.adam
- adam-cli_${scala.version.prefix}
+ adam-cli-spark2_${scala.version.prefix}
${adam.version}
org.bdgenomics.cannoli
- cannoli-core_${scala.version.prefix}
+ cannoli-core-spark2_${scala.version.prefix}
${project.version}
org.bdgenomics.cannoli
- cannoli-cli_${scala.version.prefix}
+ cannoli-cli-spark2_${scala.version.prefix}
${project.version}
org.bdgenomics.utils
- utils-misc_${scala.version.prefix}
+ utils-misc-spark2_${scala.version.prefix}
${utils.version}
test-jar
diff --git a/scripts/jenkins-test b/scripts/jenkins-test
index 24703bf..07a57e1 100755
--- a/scripts/jenkins-test
+++ b/scripts/jenkins-test
@@ -37,61 +37,6 @@ then
exit 1
fi
-# this next line is supposed to fail
-set +e
-
-echo "Rewriting POM.xml files to Scala 2.10 and Spark 1 should error..."
-./scripts/move_to_spark_1.sh
-if [[ $? == 0 ]];
-then
- echo "Running move_to_spark_1.sh when POMs are set up for Spark 1 should fail, but error code was 0 (success)."
- exit 1
-fi
-
-./scripts/move_to_scala_2.10.sh
-if [[ $? == 0 ]];
-then
- echo "Running move_to_scala_2.10.sh when POMs are set up for Scala 2.10 should fail, but error code was 0 (success)."
- exit 1
-fi
-
-set -e
-
-# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
-if [ ${SPARK_VERSION} == 2.0.0 ];
-then
-
- echo "Rewriting POM.xml files for Spark 2."
- ./scripts/move_to_spark_2.sh
-
- # shouldn't be able to move to spark 2 twice
- set +e
- ./scripts/move_to_spark_2.sh
- if [[ $? == 0 ]];
- then
- echo "We have already moved to Spark 2, so running move_to_spark_2.sh a second time should fail, but error code was 0 (success)."
- exit 1
- fi
- set -e
-fi
-
-# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
-if [ ${SCALAVER} == 2.11 ];
-then
- echo "Rewriting POM.xml files for Scala 2.11."
- ./scripts/move_to_scala_2.11.sh
-
- # shouldn't be able to move to scala 2.11 twice
- set +e
- ./scripts/move_to_scala_2.11.sh
- if [[ $? == 0 ]];
- then
- echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)."
- exit 1
- fi
- set -e
-fi
-
# print versions
echo "Testing CANNOLI version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
@@ -128,20 +73,6 @@ set -x -v
find ${CANNOLI_MVN_TMP_DIR}
rm -rf ${CANNOLI_MVN_TMP_DIR}
-# and move our poms back to their original values
-# this will allow us to pass our porcelain test at the end
-if [ ${SPARK_VERSION} == 2.0.0 ];
-then
-
- echo "Rewriting POM.xml files back to Spark 1."
- ./scripts/move_to_spark_1.sh
-fi
-if [ ${SCALAVER} == 2.11 ];
-then
- echo "Rewriting POM.xml files back to Scala 2.10."
- ./scripts/move_to_scala_2.10.sh
-fi
-
find . -name pom.xml \
-exec sed -i.bak \
-e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
diff --git a/scripts/move_to_scala_2.10.sh b/scripts/move_to_scala_2.10.sh
deleted file mode 100755
index e3ac681..0000000
--- a/scripts/move_to_scala_2.10.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-set +x
-
-grep "" pom.xml | grep -q 2.10
-if [[ $? == 0 ]];
-then
- echo "Scala version is already set to 2.10 (Scala artifacts have _2.10 version suffix in artifact name)."
- echo "Cowardly refusing to move to Scala 2.10 a second time..."
-
- exit 1
-fi
-
-find . -name "pom.xml" -exec sed -e "s/2.11.8/2.10.6/g" \
- -e "/bdg-utils.version/! s/2.11/2.10/g" -i.2.10.bak \
- -e "/no Scala/ s/Scala 2.10/Scala 2.11/g" -i.2.10.bak \
- '{}' \;
-find . -name "*.2.10.bak" -exec rm -f {} \;
diff --git a/scripts/move_to_spark_1.sh b/scripts/move_to_spark_1.sh
deleted file mode 100755
index e20b865..0000000
--- a/scripts/move_to_spark_1.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-set +x
-
-grep -q "spark2" pom.xml
-if [[ $? == 1 ]];
-then
- echo "POM is already set up for Spark 1 (Spark 1/2 artifacts are missing -spark2 suffix in artifact names)."
- echo "Cowardly refusing to move to Spark 1 a second time..."
-
- exit 1
-fi
-
-find . -name "pom.xml" -exec sed \
- -e "s/-spark2//g" \
- -e "/spark.version/ s/2.1.0/1.6.3/g" \
- -i.spark1.bak '{}' \;
diff --git a/scripts/release/release.sh b/scripts/release/release.sh
index 8632f33..8b1dc18 100755
--- a/scripts/release/release.sh
+++ b/scripts/release/release.sh
@@ -24,64 +24,6 @@ echo "releasing from ${commit} on branch ${branch}"
git push origin ${branch}
-# do scala 2.10 release
-git checkout -b maint_2.10-${release} ${branch}
-mvn --batch-mode \
- -P distribution \
- -Dresume=false \
- -Dtag=cannoli-parent_2.10-${release} \
- -DreleaseVersion=${release} \
- -DdevelopmentVersion=${devel} \
- -DbranchName=cannoli_2.10-${release} \
- release:clean \
- release:prepare \
- release:perform
-
-if [ $? != 0 ]; then
- echo "Releasing Spark 1, Scala 2.10 version failed."
- exit 1
-fi
-
-# do scala 2.11 release
-git checkout -b maint_2.11-${release} ${branch}
-./scripts/move_to_scala_2.11.sh
-git commit -a -m "Modifying pom.xml files for Spark 1, Scala 2.11 release."
-mvn --batch-mode \
- -P distribution \
- -Dresume=false \
- -Dtag=cannoli-parent_2.11-${release} \
- -DreleaseVersion=${release} \
- -DdevelopmentVersion=${devel} \
- -DbranchName=cannoli_2.11-${release} \
- release:clean \
- release:prepare \
- release:perform
-
-if [ $? != 0 ]; then
- echo "Releasing Spark 1, Scala 2.11 version failed."
- exit 1
-fi
-
-# do spark 2, scala 2.10 release
-git checkout -b maint_spark2_2.10-${release} ${branch}
-./scripts/move_to_spark_2.sh
-git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.10 release."
-mvn --batch-mode \
- -P distribution \
- -Dresume=false \
- -Dtag=cannoli-parent-spark2_2.10-${release} \
- -DreleaseVersion=${release} \
- -DdevelopmentVersion=${devel} \
- -DbranchName=cannoli-spark2_2.10-${release} \
- release:clean \
- release:prepare \
- release:perform
-
-if [ $? != 0 ]; then
- echo "Releasing Spark 2, Scala 2.10 version failed."
- exit 1
-fi
-
# do spark 2, scala 2.11 release
git checkout -b maint_spark2_2.11-${release} ${branch}
./scripts/move_to_spark_2.sh